Re: [Apbs-users] Error parsing atom in binary package

[Nathan B. <ba...@bi...>]

Hello --

You'll need to provide your input file so we can examine it for syntax  
errors.

Thanks,

Nathan

On Jul 6, 2009, at 11:14 AM, Tran Duc Trinh wrote:

> Hello all,
> I tried to install apbs 0.5.1 on a linux supported cluster, however,  
> after installing i tried to run an example from the package but  
> there is error message.
>
> "Parsing input file apbs-smpbe-24dup.in...
> NOsh:  Read non-float (charge) while parsing ION keyword!
> Error while parsing input file."
>
> Can anyone tells me what is the cause of the problem and how to fix  
> that?
> Thank you very much,
> -Trinh
>
>
>
> +++++++++++++++++++
>
> Life may be hard on you.
> Do not blame anyone but try your best.
>
>
> --- On Thu, 7/2/09, Nathan Baker <ba...@bi...> wrote:
>
> From: Nathan Baker <ba...@bi...>
> Subject: Re: [Apbs-users] Error parsing atom in binary package
> To: "Tran Duc Trinh" <tra...@ya...>
> Cc: "Yong Huang" <yhu...@gm...>, apbs- 
> us...@li...
> Date: Thursday, July 2, 2009, 7:37 PM
>
> Hello --
>
> Could you please send your PQR file so we can get a better idea of  
> what the cause of the problem might be?
>
> Thanks,
>
> Nathan
>
> On Thu, Jul 2, 2009 at 5:58 PM, Tran Duc Trinh  
> <tra...@ya...> wrote:
> I am new to apbs and currently using the binary package for Windows  
> on my desktop. It works very good for small molecule, however it  
> reported problem "Error parsing atom #" for bigger problem.
> I think that my be because of the limitation in the number of atoms  
> of the binary package for Windows. Can anyone tells me what is the  
> maximum number of atoms for binary package? My macromolecule has  
> more than 50000 atoms. Any help to overcome the problem is very  
> appreciated.
> Thanks,
> Trinh
>
>
>
>
> +++++++++++++++++++
>
> Life may be hard on you.
> Do not blame anyone but try your best.
>
>
> --- On Thu, 7/2/09, Yong Huang <yhu...@gm...> wrote:
>
> From: Yong Huang <yhu...@gm...>
> Subject: Re: [Apbs-users] Pymol APBS plugin (Was: cpp sanity)
> To: "Nathan I Nicely" <nat...@du...>
> Cc: apb...@li...
> Date: Thursday, July 2, 2009, 9:35 AM
>
> Hello,
>
> Actually if you use PDB2PQR (http://pdb2pqr.sourceforge.net/) to  
> prepare your pqr, then open this pqr file in PyMOL APBS Tools, there  
> won't be such a b-factor issue.
>
> Thanks,
>
> Yong
>
>
> On Thu, Jul 2, 2009 at 8:29 AM, Nathan I Nicely <nat...@du... 
> > wrote:
>
> I find the error doesn't occur with all pdb files.  For instance, it  
> occurs with 1HEW but not 1TJG.
>
> I'm using Pymol (linux) 1.1r1.  I also downgraded to Pymol (linux)  
> 0.99rc6 and saw the same behavior.  Here is the error (when it  
> occurs):
>
> Error: 1
> ValueError Exception in Tk callback
>   Function: <function <lambda> at 0xf419cb8c> (type: <type  
> 'function'>)
>   Args: ()
> Traceback (innermost last):
>   File "/usr/local/cryst/pymol/ext/lib/python2.4/site-packages/Pmw/ 
> Pmw_1_2/lib/PmwBase.py", line 1747, in __call__
>     return apply(self.func, args)
>   File "/usr/local/cryst/pymol/ext/lib/python2.4/site-packages/Pmw/ 
> Pmw_1_2/lib/PmwDialog.py", line 153, in <lambda>
>     command=lambda self=self, name=name: self._doCommand(name))
>   File "/usr/local/cryst/pymol/ext/lib/python2.4/site-packages/Pmw/ 
> Pmw_1_2/lib/PmwDialog.py", line 132, in _doCommand
>     return command(name)
>   File "/usr/local/cryst/pymol/./modules/pmg_tk/startup/ 
> apbs_tools.py", line 1111, in execute
>     self.runPsize()
>   File "/usr/local/cryst/pymol/./modules/pmg_tk/startup/ 
> apbs_tools.py", line 1155, in runPsize
>     size.runPsize(pdb_filename)
>   File "/usr/local/cryst/apbs1.1.0/share/tools/manip/psize.py", line  
> 247, in runPsize
>     self.parseInput(filename)
>   File "/usr/local/cryst/apbs1.1.0/share/tools/manip/psize.py", line  
> 88, in parseInput
>     self.parseLines(file.readlines())
>   File "/usr/local/cryst/apbs1.1.0/share/tools/manip/psize.py", line  
> 99, in parseLines
>     self.q = self.q + float(words[3])
> ValueError: invalid literal for float(): 1.00116.86
>
> That final float value changes a little depending on which pdb file  
> I try.
>
> Nate N.
>
>
>
> David Gohara <sd...@gm...>
> 07/01/2009 05:01 PM
> To
> Nathan I Nicely <nat...@du...>
> cc
> Nathan Baker <ba...@bi...>, apb...@li...
> Subject
> Re: [Apbs-users] Pymol APBS plugin (Was: cpp sanity)
>
>
>
>
>
>
>
> Hi Nathan,
>
>  What version of PyMol are you currently using?
>
> Dave
>
> On Wed, Jul 1, 2009 at 3:54 PM, Nathan I  
> Nicely<nat...@du...> wrote:
> >
> > Yes, that issue was resolved.  It was a problem in the interface  
> between the
> > chair and the keyboard.
> >
> > Though now I'm having issues with the APBS plugin in Pymol.  'Set  
> grid'
> > throws some tk errors of which I can't make sense.  My workaround  
> is to
> > upload my pdbs to the PDB2PQR server and check the 'generate APBS  
> input'
> > box, then run APBS with that script on the command line, then load  
> pot.dx in
> > Pymol.  I notice that trying to load subsequent surfaces causes  
> problems
> > with the display of previously loaded surfaces?
> >
> > Nate N.
> >
> >
> >
> > Nathan Baker <ba...@bi...>
> > Sent by: Nathan Baker <sob...@gm...>
> >
> > 07/01/2009 04:34 PM
> >
> > To
> > Nathan I Nicely <nat...@du...>
> > cc
> > apb...@li...
> > Subject
> > Re: [Apbs-users] cpp sanity error in compiling apbs
> >
> >
> >
> >
> > Hello --
> >
> > Your messages to the mailing list arrived out of order; is this  
> the problem
> > that you've already found a solution to?
> >
> > Thanks,
> >
> > Nathan
> >
> > On Jul 1, 2009, at 8:32 AM, Nathan I Nicely wrote:
> >
> > I've tried to install APBS on two different computers this morning  
> and both
> > times I got the following error:
> >
> > configure: error: C++ preprocessor "/lib/cpp" fails sanity check
> >
> > The only thing the two computers have in common is that they both  
> run Ubuntu
> > 9.04 with kernel 2.6.28-13.  One is a 32bit laptop, and the other  
> is dual
> > processor 64bit.  I don't know enough about programming to include  
> other
> > relevant information, I'm afraid.  I'd appreciate any help in  
> resolving this
> > error.
> >
> > Nate N.
> >  
> ------------------------------------------------------------------------------
> > _______________________________________________
> > apbs-users mailing list
> > apb...@li...
> > https://lists.sourceforge.net/lists/listinfo/apbs-users
> >
> > --
> > Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> > Director, Computational and Molecular Biophysics Graduate Program
> > Center for Computational Biology, Washington University in St. Louis
> > Web: http://bakergroup.wustl.edu/
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >  
> ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > apbs-users mailing list
> > apb...@li...
> > https://lists.sourceforge.net/lists/listinfo/apbs-users
> >
> >
>
>
>
> -- 
> Department of Biochemistry and Molecular Biophysics
> Center for Computational Biology
> Washington University School of Medicine
> St. Louis, MO
>
> http://www.macresearch.org
> http://gohara.wustl.edu
>
> 314-362-1583 (phone)
> 617-216-8616 (cell)
>
>
> ------------------------------------------------------------------------------
>
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> apb...@li...
> https://lists.sourceforge.net/lists/listinfo/apbs-users
>
>
>
>
> -- 
> Yong Huang, D.Sc.
>
> Center for Computational Biology
> Washington University School of Medicine
>
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>
> _______________________________________________
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> apb...@li...
> https://lists.sourceforge.net/lists/listinfo/apbs-users
>
>
>
>
> -- 
> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> Director, Computational and Molecular Biophysics Graduate Program
> Center for Computational Biology, Washington University in St. Louis
> Web: http://bakergroup.wustl.edu/
>

--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis
Web: http://bakergroup.wustl.edu/